aee: Ancestral Expression Estimation

In jingwyang/TreeExp: the R package for analyzing expression evolution based on RNA-seq data

Description

This function esitmates ancestral expression profile and related statistical uncertainty

Usage

aee(x, phy, mat, CI = TRUE)

Arguments

x	a vector of known expression profile, preferably log-transformed expression levels (e.g. log RPKM)
phy	an unrooted phylogenetic tree in the form of class "phylo"
mat	a matrix generated from "varMatInv" function
CI	a logical specifying whether to return the 95 intervals of the estimated ancestral expression levels

Value

returns a list containing estimated ancestral expression profile as well as other requested parameters

Examples

library('ape')
data('tetraExp')
dismat <- expdist(tetraExp, taxa = "all", subtaxa = "Brain", method = "sou")
exp_tree <- NJ(dismat)
exp_tree <- no0br(exp_tree)
var_mat <- varMatInv(objects = tetraExp,phy = exp_tree,taxa = "all",
subtaxa = "Brain")
exp_table <- exptabTE(tetraExp, taxa = "all", subtaxa = "Brain")
exp_one <- aee(exp_table[1,], exp_tree, var_mat)
exp_tree$node.label <- exp_one$est
exp_tree <- root(exp_tree, outgroup = "Chicken_Brain",
resolve.root = TRUE)
plot(exp_tree,show.node.label = TRUE)

jingwyang/TreeExp documentation built on June 11, 2019, 6:17 p.m.